8ovd: Difference between revisions

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-'''Unreleased structure'''
-The entry 8ovd is ON HOLD
+==Respiratory supercomplex (III2-IV2) from Mycobacterium smegmatis==
+<StructureSection load='8ovd' size='340' side='right'caption='[[8ovd]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[8ovd]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycolicibacterium_smegmatis Mycolicibacterium smegmatis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8OVD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8OVD FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3PE:1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE'>3PE</scene>, <scene name='pdbligand=7PH:(1R)-2-(DODECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL+TETRADECANOATE'>7PH</scene>, <scene name='pdbligand=9XX:(2S)-1-(hexadecanoyloxy)propan-2-yl+(10S)-10-methyloctadecanoate'>9XX</scene>, <scene name='pdbligand=9YF:(2R)-2-(hexadecanoyloxy)-3-{[(S)-hydroxy{[(1R,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl+(9S)-9-methyloctadecanoate'>9YF</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CDL:CARDIOLIPIN'>CDL</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=HEA:HEME-A'>HEA</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=IZL:[(2~{R})-3-[[(1~{S},2~{R},3~{S},4~{S},5~{R},6~{R})-2-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-[[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-[[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-4,5-bis(oxidanyl)oxan-2-yl]oxymethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxymethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4,5-tris(oxidanyl)-6-[(2~{R},3~{S},4~{S},5~{S},6~{R})-3,4,5-tris(oxidanyl)-6-(undecanoyloxymethyl)oxan-2-yl]oxy-cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-2-undecanoyloxy-propyl]+(10~{R})-10-methyldodecanoate'>IZL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MQ9:MENAQUINONE-9'>MQ9</scene>, <scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</scene>, <scene name='pdbligand=TRD:TRIDECANE'>TRD</scene>, <scene name='pdbligand=WUO:acyl-phosphatidyl-myo-inositol+dimannoside+(AcPIM2)'>WUO</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=8ovd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8ovd OCA], [https://pdbe.org/8ovd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8ovd RCSB], [https://www.ebi.ac.uk/pdbsum/8ovd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8ovd ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/A0R052_MYCS2 A0R052_MYCS2]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Aerobic life is powered by membrane-bound redox enzymes that shuttle electrons to oxygen and transfer protons across a biological membrane. Structural studies suggest that these energy-transducing enzymes operate as higher-order supercomplexes, but their functional role remains poorly understood and highly debated. Here we resolve the functional dynamics of the 0.7 MDa III(2)IV(2) obligate supercomplex from Mycobacterium smegmatis, a close relative of M. tuberculosis, the causative agent of tuberculosis. By combining computational, biochemical, and high-resolution (2.3 A) cryo-electron microscopy experiments, we show how the mycobacterial supercomplex catalyses long-range charge transport from its menaquinol oxidation site to the binuclear active site for oxygen reduction. Our data reveal proton and electron pathways responsible for the charge transfer reactions, mechanistic principles of the quinone catalysis, and how unique molecular adaptations, water molecules, and lipid interactions enable the proton-coupled electron transfer (PCET) reactions. Our combined findings provide a mechanistic blueprint of mycobacterial supercomplexes and a basis for developing drugs against pathogenic bacteria.
-Authors:
+Long-range charge transfer mechanism of the III(2)IV(2) mycobacterial supercomplex.,Riepl D, Gamiz-Hernandez AP, Kovalova T, Krol SM, Mader SL, Sjostrand D, Hogbom M, Brzezinski P, Kaila VRI Nat Commun. 2024 Jun 20;15(1):5276. doi: 10.1038/s41467-024-49628-9. PMID:38902248<ref>PMID:38902248</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 8ovd" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Mycolicibacterium smegmatis]]
+[[Category: Brzezinski P]]
+[[Category: Gamiz-Hernandez A]]
+[[Category: Hogbom M]]
+[[Category: Kaila V]]
+[[Category: Kovalova T]]
+[[Category: Krol S]]
+[[Category: Riepl D]]
+[[Category: Sjostrand D]]